Journal article
Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives
Bioinformatics (Oxford, England), Vol.30(15), pp.2189-2196
08/01/2014
DOI: 10.1093/bioinformatics/btu198
PMCID: PMC4103601
PMID: 24740360
Abstract
Family-based designs are regaining popularity for genomic sequencing studies because they provide a way to test cosegregation with disease of variants that are too rare in the population to be tested individually in a conventional case-control study.
Where only a few affected subjects per family are sequenced, the probability that any variant would be shared by all affected relatives-given it occurred in any one family member-provides evidence against the null hypothesis of a complete absence of linkage and association. A P-value can be obtained as the sum of the probabilities of sharing events as (or more) extreme in one or more families. We generalize an existing closed-form expression for exact sharing probabilities to more than two relatives per family. When pedigree founders are related, we show that an approximation of sharing probabilities based on empirical estimates of kinship among founders obtained from genome-wide marker data is accurate for low levels of kinship. We also propose a more generally applicable approach based on Monte Carlo simulations. We applied this method to a study of 55 multiplex families with apparent non-syndromic forms of oral clefts from four distinct populations, with whole exome sequences available for two or three affected members per family. The rare single nucleotide variant rs149253049 in ADAMTS9 shared by affected relatives in three Indian families achieved significance after correcting for multiple comparisons ([Formula: see text]).
Source code and binaries of the R package RVsharing are freely available for download at http://cran.r-project.org/web/packages/RVsharing/index.html.
alexandre.bureau@msp.ulaval.ca or ingo@jhu.edu
Supplementary data are available at Bioinformatics online.
Details
- Title: Subtitle
- Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives
- Creators
- Alexandre Bureau - Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi ArabiaCentre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi ArabiaSamuel G Younkin - Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi ArabiaMargaret M Parker - Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi ArabiaJoan E Bailey-Wilson - Vanderbilt UniversityMary L Marazita - University of PittsburghJeffrey C Murray - University of Iowa, Dental ResearchElisabeth Mangold - Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi ArabiaHasan Albacha-Hejazi - Université LavalTerri H Beaty - Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi ArabiaIngo Ruczinski - Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, G1J 2G3, Département de Médecine Sociale et Préventive, Université Laval, Québec, G1V 0A6 Canada, Department of Biostatistics, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA 15219, Department of Pediatrics, School of Medicine, University of Iowa, IA 52242, USA, Institute of Human Genetics, University of Bonn, Bonn D-53127, Germany and Dr. Hejazi Clinic, P.O. Box 2519, Riyadh 11461, Saudi Arabia
- Resource Type
- Journal article
- Publication Details
- Bioinformatics (Oxford, England), Vol.30(15), pp.2189-2196
- DOI
- 10.1093/bioinformatics/btu198
- PMID
- 24740360
- PMCID
- PMC4103601
- NLM abbreviation
- Bioinformatics
- ISSN
- 1367-4803
- eISSN
- 1367-4811
- Grant note
- U01 DE020073 / NIDCR NIH HHS R01-DE009886 / NIDCR NIH HHS R01 DE016148 / NIDCR NIH HHS R37-DE008559 / NIDCR NIH HHS U01 DE018993 / NIDCR NIH HHS R10-DE-014581 / NIDCR NIH HHS X01-HG006177 / NHGRI NIH HHS R01 DE014581 / NIDCR NIH HHS R01 GM083084 / NIGMS NIH HHS R37 DE008559 / NIDCR NIH HHS U01 DE020057 / NIDCR NIH HHS R01-DE016148 / NIDCR NIH HHS R01 DE009886 / NIDCR NIH HHS
- Language
- English
- Date published
- 08/01/2014
- Academic Unit
- Anatomy and Cell Biology; Stead Family Department of Pediatrics; Epidemiology; Pediatric Dentistry; Craniofacial Anomalies Research Center; Dental Research
- Record Identifier
- 9984025461902771
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